title: Attachment site recognition and regulation of directionality by the serine integrases.
abstract: Serine integrases catalyze the integration of bacteriophage DNA into a host genome by site-specific recombination between 'attachment sites' in the phage (attP) and the host (attB). The reaction is highly directional; the reverse excision reaction between the product attL and attR sites does not occur in the absence of a phage-encoded factor, nor does recombination occur between other pairings of attachment sites. A mechanistic understanding of how these enzymes achieve site-selectivity and directionality has been limited by a lack of structural models. Here, we report the structure of the C-terminal domains of a serine integrase bound to an attP DNA half-site. The structure leads directly to models for understanding how the integrase-bound attP and attB sites differ, why these enzymes preferentially form attP × attB synaptic complexes to initiate recombination, and how attL × attR recombination is prevented. In these models, different domain organizations on attP vs. attB half-sites allow attachment-site specific interactions to form between integrase subunits via an unusual protruding coiled-coil motif. These interactions are used to preferentially synapse integrase-bound attP and attB and inhibit synapsis of integrase-bound attL and attR. The results provide a structural framework for understanding, testing and engineering serine integrase function.
authors.affiliation: Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA and NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Building 436E, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, IL 60439, USA.
authors.forename: Karen
authors.initials: K
authors.lastname: Rutherford
authors.forename: Peng
authors.initials: P
authors.lastname: Yuan
authors.forename: Kay
authors.initials: K
authors.lastname: Perry
authors.forename: Robert
authors.initials: R
authors.lastname: Sharp
authors.forename: Gregory D
authors.initials: GD
authors.lastname: Van Duyne
mesh_terms: D000595:Amino Acid Sequence; D001287:Attachment Sites, Microbiological; D001435:Bacteriophages / Q000201:enzymology; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D019426:Integrases / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D011995:Recombination, Genetic; D016415:Sequence Alignment; D012694:Serine / Q000737:chemistry
chemical_list: D012694:Serine; D004247:DNA; D019426:Integrases